analysis of ITS2


I have ITS2 dataset generated by MiSeq to analyze but I am very new to this area of research. I have so far followed MiSeq SOP for 16S, but I am currently stuck. I understand that I have to use UNITE for ITS2 instead of Silva, but what command shall I run since UNITE is not aligned? Can I use classify.seqs to replace align.seqs? And could anyone please help to brief the steps for ITS2 that are different from those for 16S in the SOP?

Thank you in advance for all suggestions!

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